Improvements and ideologies that give percentage bonuses do not just increase your base values, but also any penalties. This results in that these improvements become useless or even harmful when the penalties are large.

Example the Large empire penalty:

Supportive Population (+4), Colony Capital (+3), 2x Entertainment Center (+3), Civilization Capital Bonus (+2), Intimidation Center (+50%), 3x Zero G Ballet (+3), Large empire penalty (110x 0.2), 30 Population.

Gives an approval of 10.0% ([4+3+2x3+2+3x3-110x0.2] * 1.5 / 30) while you would expect 46.7% ([[4+3+2x3+2+3x3] * 1.5 - 110x0.2] / 30)

The problem lies in the fact that the penalty is applied before the percentual bonuses.

It might be as designed, but on the larger maps it really hurts you.